BAC - Automated Binding Affinity Calculations Sample Clauses

BAC - Automated Binding Affinity Calculations. The Binding Affinity Calculator (BAC) is a decision support tool which uses molecular level computer simulation to reliably predict the binding affinities (free energies) of molecules with target proteins, and therefore to identify those most likely to bind to the protein. BAC has been built to integrate and automate the multi-step process of model building, simulation and data analysis for molecular level drug-receptor interactions7,8. It constitutes a sophisticated computational pipeline built from selected software tools and services, and which relies on access to a range of computational resources. Ultimately, one important use is a more accurate computational design of candidate drug molecules. In fact, BAC is currently in use with a number of pharma companies. BAC depends on the ability to perform hundreds of separate parallel simulations on a high- performance computing platform, each of which can require 50-200 cores depending on the system. The BAC workflow automates much of the complexity of running and marshalling these simulations, and collecting and analysing data. BAC constitutes a workflow of operations encompassing several different binaries along with data creation and transformation scripts. It can be deployed in multiple application scenarios, but is principally used as either a direct ‘application’ run by a researcher on an HPC platform (which depends on significant HPC experience in order to use successfully), or more latterly in a Software as a Service model, where the deployment is taken care of on a user’s behalf, and they actually run BAC via a web interface. UF-BAC is a web portal based interface to the binding affinity calculator (BAC), which allows a user to build models of molecule-compound binding, and execute and analyse multi-replica molecular dynamics (MD) simulations using the model. The binding affinity may be calculated by ESMACS or TIES methods. UF-BAC enables BAC to be run via a Software as a Service model, hiding from the user the complexities of the command line tools used to build models, execute them on compute resources, and analyse the results. UF-BAC is the interface to BAC and is required to run the BAC application.
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